Let’s examine the parts with Natives. Fortunately, they're in only two brief scenes. (Which explains why they weren’t featured in the trailer.) This is fortunate because the two scenes are purely stereotypical.
Monkey see, monkey fu
In ruins outside the town of Nazca, Indiana and Mutt are attacked by three lurking Indians. These Indians climb and scamper like monkeys. In fact, when we first see them, we’re not sure if they’re human or not.
It turns out they know monkey fu (monkey-style kung fu), a martial art involving rapid leg kicks. They wear skull-faced masks. And they use blowguns as weapons.
These Indians aren’t guarding the ruins for any particular reason. They're just doing what movie Indians do--namely, skulking and attacking from the shadows. It's almost literally a case of "monkey see, monkey do": Monkey-like Indians see victims, monkey-like Indians do victims.
The scene is set in Peru's arid coastal region, far from the Amazon jungle. It's unlikely these Indians came from distant Akator, the kingdom of the crystal skull. Moreover, they're wearing regular clothes. So what are they doing there?
And why are they using blowguns? Was the local pawn shop out of guns, machetes, knives, or anything made of metal? As Indiana soon demonstrates, blowguns aren't the best weapon to use in hand-to-hand combat.
To sum it up, the ape-like behavior suggests the Indians are subhuman. The masks suggest they’re evil. And the blowguns suggest they’re primitive. Nice.
In the lost city of Akator, Indiana and company are attacked by more skulking Indians. These bogeymen drop from their hiding places and stalk our heroes like panthers--crouching because beast-like Indians don't walk or run upright.
Unlike the previous posers, these savages are the real deal. They’re half-naked. They wield spears, blowguns, and bolas. They wear necklaces and earrings of claws or bones. They have dark makeup around their eyes and scarification marks on their skin. Some are daubed with mud, making them look deathly pale. Their heads are shaved, generally the mark of an evil Indian, with scary-clown sprays of hair. About the only thing missing is garish warpaint and nose rings.
Why do these Indians attack? The movie doesn't give a reason. We know the temple isn’t theirs because the skull beings built it. The Indians may be guarding the skulls, but there's no proof of that. It's not clear they even know about the skulls, since the objects are locked in a hidden chamber.
But these Indians don't need a motive. They’re your basic skulking savages. They live and die to capture and kill.
The attack is cut short when the Communists arrive. They mow down the Indians in a hail of lead. And...that’s it for the Indians.
Since no other Indians appear, we can surmise the Commies have wiped out the entire tribe. That would make them guilty of genocide. But do they care? Does anyone?
Certainly Indiana Jones and company, those heralds of Western civilization, don't. They don't give a thought to the anonymous corpses lying about. The Indians attacked them and now they’re dead. That’s all that matters.
Of course, these Indians were just defending their heritage. Even if they didn’t claim the kingdom as their own, they presumably had rights to the territory. But the Westerners regard them about the way they regard army ants: as pests to be avoided or exterminated. Nice.
P.S. I didn’t catch the name of this tribe in the movie, but the Indiana Jones wiki says it’s Ugha. Are you kidding me? "Ugha" as in "ugh, a bunch of savages"? Needless to say, this is a stupid and insulting name for an Amazon Indian tribe. Even if it's based on something, Spielberg should've changed it.
For more on the subject, see Indiana Jones and the Stereotypes of Doom.